A rocket was intercepted by Israel's Iron Dome anti-missile defense system, while the rest fell in open fields, reported Xinhua citing Israel's Channel 2.
Hamas' military wing Izz ad-Din al-Qassam Brigades claimed responsibility for the attack, saying they launched three M-75 missiles targeting the reactor in Dimona.
It's the first time that rockets have hit Dimona, one of Israel 's most sensitive areas.
Prime Minister Benjamin Netanyahu has said Israel will further intensify its offensive on Gaza.
"We have decided to further increase our attacks against Hamas and other terrorist organisations in the Gaza Strip," Netanyahu said, swearing that Hamas "will pay a heavy price" for the barrages of rockets launched from the Gaza Strip towards Israel.
Since Israel launched military operation Protective Edge early Tuesday, it has attacked over 560 sites in Gaza, killing at least 41 Palestinians, according to the army. Hamas militants have fired more than 160 rockets at Israel.